The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

• Published in: Nature communications Vol. 11; no. 1; p. 3145
• Main Authors: Schulze, Stefan, Adams, Zachary, Cerletti, Micaela, De Castro, Rosana, Ferreira-Cerca, Sébastien, Fufezan, Christian, Giménez, María Inés, Hippler, Michael, Jevtic, Zivojin, Knüppel, Robert, Legerme, Georgio, Lenz, Christof, Marchfelder, Anita, Maupin-Furlow, Julie, Paggi, Roberto A., Pfeiffer, Friedhelm, Poetsch, Ansgar, Urlaub, Henning, Pohlschroder, Mechthild
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19-06-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2784; 631/326/26/2523; 82/58; 82/81; Amino Acid Sequence; Archaea; Archaeal Proteins; Archaeal Proteins - metabolism; BASIC BIOLOGICAL SCIENCES; Biology; Cell culture; Data interpretation; Datasets as Topic; Glycosylation; Haloferax volcanii; Haloferax volcanii - physiology; Humanities and Social Sciences; Life Sciences; Mass Spectrometry; Mass spectroscopy; Metabolism; multidisciplinary; Protein turnover; Proteins; Proteome; Proteome - metabolism; Proteomes; Proteomics; Proteomics - methods; Science; Science (multidisciplinary); Terminal protein
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-16784-7

While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon
Haloferax volcanii
, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation,
N
-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
While archaeal proteomics advanced rapidly, a comprehensive proteome database for archaea is lacking. Therefore, the authors here launch the Archaeal Proteome Project, a community-effort providing insights into archaeal cell biology via the combined reanalysis of
Haloferax volcanii
proteomics data.